# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:19:56 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: ~{N},~{N}-dimethylethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(C)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 5Y9  5Y9  ~{N},~{N}-dimethylethanamide  ligand  15  6  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5Y9
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 5Y9  C01  C  CH3   0  -0.515  -1.6144   0.9280  -0.0052
 5Y9  N02  N  NT    0  -0.432  -0.6222  -0.1225   0.1052
 5Y9  C03  C  CH3   0  -0.522  -1.1355  -1.4749   0.1392
 5Y9  C04  C  C     0   0.517   0.6815   0.1880  -0.0607
 5Y9  C05  C  CH3   0  -0.802   1.6845  -0.9412  -0.0061
 5Y9  O06  O  O     0  -0.512   1.0463   1.3451  -0.2389
 5Y9  H1   H  HCH3  0   0.236  -1.8652   1.1469  -1.0462
 5Y9  H2   H  HCH3  0   0.239  -2.5232   0.6086   0.5013
 5Y9  H3   H  HCH3  0   0.249  -1.2676   1.8443   0.4650
 5Y9  H4   H  HCH3  0   0.238  -1.5576  -1.7694  -0.8251
 5Y9  H5   H  HCH3  0   0.264  -0.3634  -2.1905   0.4030
 5Y9  H6   H  HCH3  0   0.246  -1.9226  -1.5511   0.8891
 5Y9  H7   H  HCH3  0   0.265   1.5151  -1.6696  -0.7998
 5Y9  H8   H  HCH3  0   0.266   2.6848  -0.5324  -0.1216
 5Y9  H9   H  HCH3  0   0.264   1.6418  -1.4799   0.9418

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 5Y9  C03  N02  single  1.447  0.020  1.447
 5Y9  C01  N02  single  1.449  0.020  1.449
 5Y9  N02  C04  single  1.350  0.020  1.350
 5Y9  C04  O06  double  1.226  0.020  1.226
 5Y9  C04  C05  single  1.511  0.020  1.511
 5Y9  C01  H1   single  0.970  0.020  1.090
 5Y9  C01  H2   single  0.970  0.020  1.090
 5Y9  C01  H3   single  0.970  0.020  1.090
 5Y9  C03  H4   single  0.970  0.020  1.090
 5Y9  C03  H5   single  0.970  0.020  1.090
 5Y9  C03  H6   single  0.970  0.020  1.090
 5Y9  C05  H7   single  0.970  0.020  1.090
 5Y9  C05  H8   single  0.970  0.020  1.090
 5Y9  C05  H9   single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 5Y9  H3   C01  H2   108.21  3.000
 5Y9  H3   C01  H1   108.45  3.000
 5Y9  H2   C01  H1   108.08  3.000
 5Y9  H3   C01  N02  111.09  3.000
 5Y9  H2   C01  N02  108.87  3.000
 5Y9  H1   C01  N02  112.02  3.000
 5Y9  C04  N02  C03  124.08  3.000
 5Y9  C04  N02  C01  119.00  3.000
 5Y9  C03  N02  C01  115.88  3.000
 5Y9  H6   C03  H5   107.48  3.000
 5Y9  H6   C03  H4   108.02  3.000
 5Y9  H5   C03  H4   108.15  3.000
 5Y9  H6   C03  N02  109.74  3.000
 5Y9  H5   C03  N02  111.69  3.000
 5Y9  H4   C03  N02  111.60  3.000
 5Y9  O06  C04  C05  120.85  3.000
 5Y9  C05  C04  N02  117.67  3.000
 5Y9  O06  C04  N02  121.47  3.000
 5Y9  H9   C05  H8   108.31  3.000
 5Y9  H9   C05  H7   107.24  3.000
 5Y9  H8   C05  H7   108.47  3.000
 5Y9  H9   C05  C04  111.98  3.000
 5Y9  H8   C05  C04  109.02  3.000
 5Y9  H7   C05  C04  111.70  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 5Y9  CONST_01  O06  C04  N02  C01    0.00   0.0  0
 5Y9  CONST_02  C05  C04  N02  C01  180.00   0.0  0
 5Y9  CONST_03  O06  C04  N02  C03  180.00   0.0  0
 5Y9  CONST_04  C05  C04  N02  C03    0.00   0.0  0
 5Y9  Var_01    H4   C03  N02  C01   69.21  30.0  3
 5Y9  Var_02    H7   C05  C04  N02   62.04  30.0  3
 5Y9  Var_03    H1   C01  N02  C03  -87.56  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 5Y9  plan-1  C01  0.020
 5Y9  plan-1  N02  0.020
 5Y9  plan-1  C03  0.020
 5Y9  plan-1  C04  0.020
 5Y9  plan-1  C05  0.020
 5Y9  plan-1  O06  0.020

